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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattataaatgtggctgggctattacatcatcctgtactttattatctcaatcgtctaattagtaaccatcttgcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA

Basic information

species Zea mays
transcript GRMZM2G006429_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006429_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 5
------------gtgattataaatg-tggctgggctattacatcatcctg--tactttattatctcaatcgtctaattagtaaccatcttgcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA
            ||| ||  |  |  | | |    | |||| | ||   |  | ||| | |||||  ||| || || |   | ||||     |||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||||| ||||||||| ||| || | |||||||
gtagtttcacgtgtggtttcagtttcttgtttatatcttactttatatggaatgcttcactatcttgatcatccaactgagatccattcatattgtacagCAAGCACTGAAGACAAGTGGGCTGAAAGATGACACCACCTGTGTGGTTGTTGATATCATCCCATCTGATCATTCTTCAACACCTCCATCACTATCTCCAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71314548|gb|DR793896.1|DR793896
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|71759367|gb|DR957304.1|DR957304
EST:     GGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: GGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|101394555|gb|EB819212.1|EB819212
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|78543568|gb|DV621066.1|DV621066
EST:     GTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: GTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|211160527|gb|FL223273.1|FL223273
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGKTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|148940664|gb|EC885476.2|EC885476
EST:     GCAAAACTTGTTTTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: GCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|71762481|gb|DR960418.1|DR960418
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|22521667|gb|BU080478.1|BU080478
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|1546867|gb|AA054810.1|AA054810
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTG-TTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|74233457|gb|DT641371.1|DT641371
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|78123110|gb|DV541494.1|DV541494
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|26455794|gb|CA827377.1|CA827377
EST:     AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
genomic: AGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC
EST: gi|67022466|gb|CO451215.1|CO451215
EST:     GGCGTGCCGGGGATTGCGTGCAGAACTGGCTGCAAAACTTGTTGTTAAG                         CAAGCTCTGAAGACAAGTGGGTTGAAAGATGATACCACATGTGTGGTTGTC
genomic: GGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 371

AATTGCATCAGATGGAATATGGGACGCTCTGTCCTCAGAGAGTGCTGCTCAGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

AATTGCATCAGATGGAATATGGGACGCTCTGTCCTCAGAGAGTGCTGCTCAGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 84

AATTGCATCAGATGGAATATGGGACGCTCTGTCCTCAGAGAGTGCTGCTCAGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

AATTGCATCAGATGGAATATGGGACGCTCTGTCCTCAGAGAGTGCTGCTCAGGCGTGCCGGGGATTACGTGCAGAACTGGCTGCAAAACTTGTTGTTAAGgtgattataa ... gcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcctgtactttattatctcaatcgtctaattagtaaccatcttgcttgtccagCAAGCTCTGAAGACAAGTGGGCTGAAAGATGACACCACATGTGTGGTTGTCGACATCATCCCATCTGATCATTGTTCAACACCACCAGCATTGTCTCCAA
                                tagtaac  putative branch site (score: 146)
                                         tcttgctt  putative PPT
          tttattatctcaat  TA-rich tract